NGE: Protocol Darkness
by mindmaster123
Summary: "An age of prosperity and scientific and technological miracles was at hand. It was a chance for peace, and for things get better for humanity. But this was all ruined at that fateful day." AU A retelling of the classic Evangelion series. Crossover with other franchises.


PROLOGUE: APOCALYPSE NOW

 _The year was 2015, during a space travel to the moon of Saturn, Titan, numerous fossilized remains and ruins were discovered, along with an object of alien origin. The artifact, dubbed "Grimoire", was a databank, the pieces of lore in it proved highly useful, thanks to its data cache, technology and science jumped years, along with mankind now knowing that they were not alone in the universe. An age of prosperity and scientific and technological miracles was at hand. It was a chance for peace, and for things get better for humanity. But this was all ruined at that fateful day._

 **South Pole, 2021**

"Doctor Katsuragi, I think we found something!" Said one of the soldiers, pointing at a purple light coming from behind a hill. Hasake Katsuragi took his notes book and he read it.

 _A few days ago, a Japanese satellite detected an anomalous surge of energy on the South Pole, a team for the Expedition was hastily gathered by the Japan Goververnment, before other countries could get a hold of whatever discovery was at hand, the leader was renowned scientist Dr. Hasake Katsuragi, a great expert on theoretical physics and energy research._

"Prepare your cameras, gentlemen." Hasake said, turning on a small rectangular device in a pocket in his right chest. "We are about to make history." The other men activated their cameras and the group walked towards the hill.

 _These men and women thought they were going to do something important. Something that would change mankind's future for the best._

A girl, about 14 years old, sprints, running past Dr. Katsuragi. "Misato, wait!" Said the man.

 _Little they knew that they were about to witness the first moments of mankind's darkest hour._

Misato climbed to the top of the hill and she looked amazed at the crater below. "Misato!" Dr. Katsuragi and the other members of the expedition reached her. "Daughter. Don't go running like this, something bad could..." Dr. Katsuragi and the others noticed what Misaot was seeing. "Happen."

In the crater below, some sort of unholy nightmare happened. Numerous humanoid creatures were performing some sort of ritual in the crater, whose ground had a large 50 miles square circle of purple flames with many alien symbols. The group took some time to look at the creatures, they all shared the characteristic of having a dry pale-white skin, some of them were bigger and wore armor and pieces of cloth, but they all invoked a feeling of undead royalty. Four humanoids that wore elaborate armor and long crumbling robes were floating meters above the circle, with their arms pointing forwards, a fifth beige one with bright blue eyes was floating in the middle with its hands clasped together and humming as if it was praying. There were other creatures around the circle, five of them were large and fully covered in heavy armor, had three bright green eyes and they yielded massive cleavers. Others, that also had three bright green eyes, wore light armor along with small cloaks and they yielded pistol like weapons. Most of them, however, were slim zombie like creatures with long arms that ended in hands with long claws, and they had dome shaped heads with no eyes. All the creatures on the ground were on their knees with their arms spread to the side and they looking at the ground, as if they were in religious reverence.

"Doc. What are those?" Asked one of the soldiers.

"There are many entries about an alien race simply known as the Hive in the Grimoire that match, at least appearance-wise, with the creatures in front of us." Dr. Katsuragi answered.

Completely oblivious to her father's explanation, Misato walked near the edge of the hill to have a better look at the ominous ritual, she ended up knocking some bits of ice and snow. One of the zombie like creatures heard that, and it rose up from its position and it looked at the top of the hill. It saw Misato and then it let out a furious high-pitched screech, all the other beings, save the floating beige one, stopped what they were doing and they readied themselves for the carnage.

The group started to walk backwards. "Run." Was what Dr. Katsuragi said. "Now!" They started to run as the creatures clawed their way up the hill. One of them aimed its pistol at Misato and shot.

 _The Hive dealt quickly with the members of the Katsuragi Expedition, who were slaughtered in a matter of minutes. But what could they do against an unknown enemy, unless perish?_

Hasake Katsuragi carried the wounded Misato back to the coast, near was the boat they used to come to the South Pole, ignoring the fact that he was bleeding profusely due to a wound in his stomach. "I think we lost them, doc." One of the remaining soldiers said as she reloaded a pistol. While panting, Hasake moved the equipment they had brought, he eventually found what he was looking for. A large white and black orb like device. "Doc...What are you doing with this Survival Pod?" The female soldier asked as Hasake put a password in the machine, that then opened.

"Doing something useful that is not related to my job." He answered as he gently put Misato inside the Pod. "We're doomed, soldier. But the least I can do is to ensure that my daughter will live." He gave the girl a necklace with an iron cross.

"Dad...What are you doing?" Misato asked weakly.

"No matter what you hear. Stay quiet." Hasake said as the pod closed.

The female soldier's right arm was torn off by a blast of electricity launched by one of the floating creatures. The army of aliens descended upon the soldiers like the ravenous beasts they were, and the soldiers were torn apart in seconds.

Doctor Hasake Katsuragi grabbed a machine gun that was on the ground, catching the attention of the creatures. One of the large cleaver-yielding ones walked closer to Hasake, intrigued at this human who stood fearless in front of them. The man opened fire at the large brute, that advanced at high speed, despite the bullets piercing its body. The monster stabbed Hasake with its cleaver, the creature lifted Hasake and stared right into his eyes before throwing him to the rest of its companions, who fell at him with a voracity. One of the zombie like creatures opened Dr Katsuraki's abdomen with its claws before starting to pull out his organs.

"Dad!" Misato covered her mouth after screaming that, still, the large creature who just killed her father heard that and it walked closer towards the Pod.

However a tower made of purple crystal took the attention of the creatures stopped what they were doing to look at it. The pillar shifted and twisted until it took the form of a giant horned humanoid with cruel purple eyes and skeletal wings. The aliens started to howl and scream in victory as the giant started to glow brighter, the titanic abomination let out a roar before it punched the ground and then it exploded.

 _The catastrophe was called "Second Impact", Japan Government created a cover up story, saying that it was a Meteorite that caused the disaster. As a result of it, the ice in the South Pole was completely molten down,_ _Two billion people in the southern hemisphere were instantly killed by the gargantuan tsunamis which followed the explosion. Many more would die in world wide coastal flooding. And then, two days later, the invasion happened. At first I didn't understand why, but now I know that they were acting on the behalf of my creator's old enemy. The Hive attacked all places around the world with a massive army, their rampaging crusade was ruthless, billions of lives perished, the streets were red with the blood of the innocents and the corpses were piled everywhere. For reasons then unknown, the Hive stopped on their carnage and left the planet, leaving the survivors to rebuild whatever they could of their home._

 _Three days. Humanity almost went extinct in three days. I wasn't allowed to do a thing to help them. I could only watch as the humans perish. I still question if I could have helped them. It is useless to just look at the past and wonder how things could have turned out. The important is this. That world was about to face its biggest crisis._

 **To Be Continue**

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 **Author's Notes:** You see. The idea for this one came after a talk I had with my friend darkmachines about the concept of multiverse, I just kept thinking about it until a few ideas popped in, such as this one. As always, review after reading, I see you guys later :)


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